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Pacureanu L, Bora A, Crisan L. New Insights on the Activity and Selectivity of MAO-B Inhibitors through In Silico Methods. Int J Mol Sci 2023; 24:ijms24119583. [PMID: 37298535 DOI: 10.3390/ijms24119583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
To facilitate the identification of novel MAO-B inhibitors, we elaborated a consolidated computational approach, including a pharmacophoric atom-based 3D quantitative structure-activity relationship (QSAR) model, activity cliffs, fingerprint, and molecular docking analysis on a dataset of 126 molecules. An AAHR.2 hypothesis with two hydrogen bond acceptors (A), one hydrophobic (H), and one aromatic ring (R) supplied a statistically significant 3D QSAR model reflected by the parameters: R2 = 0.900 (training set); Q2 = 0.774 and Pearson's R = 0.884 (test set), stability s = 0.736. Hydrophobic and electron-withdrawing fields portrayed the relationships between structural characteristics and inhibitory activity. The quinolin-2-one scaffold has a key role in selectivity towards MAO-B with an AUC of 0.962, as retrieved by ECFP4 analysis. Two activity cliffs showing meaningful potency variation in the MAO-B chemical space were observed. The docking study revealed interactions with crucial residues TYR:435, TYR:326, CYS:172, and GLN:206 responsible for MAO-B activity. Molecular docking is in consensus with and complementary to pharmacophoric 3D QSAR, ECFP4, and MM-GBSA analysis. The computational scenario provided here will assist chemists in quickly designing and predicting new potent and selective candidates as MAO-B inhibitors for MAO-B-driven diseases. This approach can also be used to identify MAO-B inhibitors from other libraries or screen top molecules for other targets involved in suitable diseases.
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Affiliation(s)
- Liliana Pacureanu
- "Coriolan Dragulescu" Institute of Chemistry, 24 Mihai Viteazu Ave., 300223 Timisoara, Romania
| | - Alina Bora
- "Coriolan Dragulescu" Institute of Chemistry, 24 Mihai Viteazu Ave., 300223 Timisoara, Romania
| | - Luminita Crisan
- "Coriolan Dragulescu" Institute of Chemistry, 24 Mihai Viteazu Ave., 300223 Timisoara, Romania
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Abstract
Interaction signatures of drug candidates are characteristic to off-target (neutral) and antitarget (negative) effects, inferring reduced efficiency, side-effects and high attrition rate. Today's retroactive scaled-down virtual screening (VS) experiments relying on benchmarking datasets are extensively involved to assess ligand enrichment in the real-world problem. In recent years, unbiased benchmarking sets turned into a tremendous need to assist virtual screening methodologies for emerging drug targets. To date, the benchmarking datasets are quite limited, whereas glycogen synthase kinase-3 (GSK-3) is not included into directories of benchmarking datasets such as DUD-e, MUV, etc. Herein we introduced our in-house algorithm to build an unbiased benchmarking dataset, including highly selective, moderately selective and nonselective inhibitors for a significant therapeutic target - GSK-3, suitable for both ligand-based and structure-based VS approaches. These datasets are unbiased in terms of physico-chemical properties and topological descriptors, as resulted from mean(ROC-AUC) leave-one-out cross-validation (LOO CV). and additional 2 D similarity search. Moreover, we investigated the gradual selectivity dataset by application of multiple 2 D similarity coefficients and distances, 3 D similarity and docking. Besides the resulted links between the enrichment of selective GSK-3 inhibitors and their chemical structures, a database of compounds and their 3 D similarity signatures including cut-off thresholds for enhanced selectivity was generated. 2 D similarity space analysis revealed that selectivity problem cannot be evaluated appropriately with 2 D similarity searching alone. The current analysis provided useful, comprehensive insights, which may facilitate the knowledge-based identification of novel selective GSK-3 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Liliana Pacureanu
- "Coriolan Dragulescu" Institute of Chemistry, Romanian Academy, Timisoara, Romania
| | - Sorin Avram
- "Coriolan Dragulescu" Institute of Chemistry, Romanian Academy, Timisoara, Romania
| | - Luminita Crisan
- "Coriolan Dragulescu" Institute of Chemistry, Romanian Academy, Timisoara, Romania
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Crisan L, Avram S, Kurunczi L, Pacureanu L. Partial Least Squares Discriminant Analysis and 3D Similarity Perspective Applied to Analyze Comprehensively the Selectivity of Glycogen Synthase Kinase 3 Inhibitors. Mol Inform 2020; 39:e1900142. [PMID: 31944600 DOI: 10.1002/minf.201900142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/25/2019] [Indexed: 01/25/2023]
Abstract
The current work was conducted to investigate the effectiveness of two conceptually distinct in silico ligand-based tools: Partial Least Squares Discriminant Analysis (PLS-DA) and 3D similarity, including shape, physico-chemical and electrostatics to classify target-specific pharmacophores with enrichment power for selective GSK-3 inhibitors against the phylogenetically related CDK-2, CDK-4, CDK-5 and PKC. All virtual screens were performed on four data sets of targets matched pairwise, including selective and nonselective inhibitors for GSK-3. The classification method PLS-DA results revealed that all obtained models are statistically robust according to the cross-validation and response permutation tests. Regarding selective GSK-3 inhibitors differentiation in terms of selectivity (Se), specificity (Sp), and accuracy (ACC), the PLS-DA models for CDK-4/GSK-3, and PKC/GSK-3 datasets are highly efficient discriminative. 3D similarity searches for CDK-4/GSK-3, PKC/GSK-3, and CDK-2/GSK-3 datasets using the most selective reference molecules lead to highest enrichments of selective GSK-3 inhibitors. EON yields excellent early and overall enrichments for ET_ST and ET_combo for most selective query for CDK-4/GSK-3. CDK-5/GSK-3 dataset didn't show consistent statistically significant enrichments for 3D similarity virtual screening. The current methodology is reliable and could be used as a powerful tool for the detection of potentially selective molecules targeting GSK-3.
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Affiliation(s)
- Luminita Crisan
- "Coriolan Dragulescu" Institute of Chemistry, Romanian Academy, 24 Mihai Viteazul Ave., 300223, Timisoara, Romania
| | - Sorin Avram
- "Coriolan Dragulescu" Institute of Chemistry, Romanian Academy, 24 Mihai Viteazul Ave., 300223, Timisoara, Romania
| | - Ludovic Kurunczi
- "Coriolan Dragulescu" Institute of Chemistry, Romanian Academy, 24 Mihai Viteazul Ave., 300223, Timisoara, Romania
| | - Liliana Pacureanu
- "Coriolan Dragulescu" Institute of Chemistry, Romanian Academy, 24 Mihai Viteazul Ave., 300223, Timisoara, Romania
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Crisan L, Varga D, Pacureanu L. Pharmacophore Modeling and Docking Study of Pyrazolylaminoquinazoline Derivatives as Highly Potent Fibroblast Growth Factor Receptor Inhibitors2 (FGFR2). Rev Chim 2019. [DOI: 10.37358/rc.19.3.7008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this study pharmacophore modeling and molecular docking investigations have been performed on pyrazolylaminoquinazoline derivatives, highly potent fibroblast growth factor receptor2 (FGFR2) inhibitors. The best pharmacophore hypotheses displaying five features (ADHRR.2051 and AADHR.798) were generated using a set of 28 compounds. The associated 3D atom-based quantitative structure � activity relationships (QSAR) models were statistically robust showing high correlation coefficients (R-squared = 0.981 / 0.982), and cross validation coefficients (Q-squared = 0.645 / 0.671). The R-Pearson values for the test set of 0.805 / 0.820 indicate that the models are robust and exhibit good predictive power. The interactions of pyrazolylaminoquinazoline with FGFR2 binding site revealed two hydrogen bonds with Ala567. The obtained pharmacophore, 3D atom-based QSAR models and binding features resulted from docking studies can help medicinal chemists to design new pyrazolylaminoquinazoline inhibitors with improved potency.
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Pacureanu L, Avram S, Bora A, Kurunczi L, Crisan L. Portraying the selectivity of GSK-3 inhibitors towards CDK-2 by 3D similarity and molecular docking. Struct Chem 2018. [DOI: 10.1007/s11224-018-1224-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Buiu C, Avram S, Duda-Seiman D, Milac AL, Duda-Seiman C, Pacureanu L, Borcan F. More effective DPP4 inhibitors as antidiabetics based on sitagliptin applied QSAR and clinical methods. Curr Comput Aided Drug Des 2015; 10:237-49. [PMID: 25756669 DOI: 10.2174/157340991003150302230811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 07/03/2014] [Accepted: 07/27/2014] [Indexed: 11/22/2022]
Abstract
Xanthine-based molecules such as serine protease dipeptidyl peptidase 4 (DPP4) inhibitors are compounds often used in improving glycemic control in type 2 diabetic patients and also used for their effects as mild stimulants and as bronchodilators, notably in treating asthma symptoms. Here, we aim to better understand the molecular features affecting activity of xanthine-based DPP4 inhibitors such as sitagliptin and related compounds and use these features to de novo predict improved sitagliptin derivatives. To this end, we performed a clinical study to examine the efficacy and safety of once-daily 100 mg oral sitagliptin as monotherapy in Romanian patients with type 2 diabetes. This study indicates that sitagliptin effectively decreases the glycemic level and provides very good glycemic equilibrium. To predict putative new drugs with identical pharmacological effects at lower dosages, we generate QSAR models based on compound series containing 35 DPP4 inhibitors. We establish that the physicochemical parameters critical for DPP4 inhibitory activity are: hydrophobicity described by the logarithm of the octanol/water partition coefficient, counts of rotatable bonds, hydrogen bond donor and acceptor atoms, and topological polar surface area. The predictive power of our QSAR models is indicated by significant values of statistical coefficients: cross-validated correlation q2 (0.77), fitted correlation coefficient r2 (0.85) and standard error of prediction (0.34). Based on the established QSAR equations, we propose and analyse 19 new sitagliptin derivatives with possibly improved pharmacological effect as DPP4 inhibitors.
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Affiliation(s)
| | | | | | - Adina L Milac
- Institute of Biochemistry of the Romanian Academy,296th Independentei Str., Bucharest-060031, Romania.
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Crisan L, Pacureanu L, Avram S, Bora A, Avram S, Kurunczi L. PLS and shape-based similarity analysis of maleimides--GSK-3 inhibitors. J Enzyme Inhib Med Chem 2013; 29:599-610. [PMID: 24047148 DOI: 10.3109/14756366.2013.833196] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
CONTEXT Glycogen synthase kinase-3 (GSK-3) overactivity was correlated with several pathologies including type 2 diabetes mellitus, Alzheimer's disease, cancer, inflammation, obesity, etc. OBJECTIVE The aim of the current investigation was to model the inhibitory activity of maleimide derivatives--inhibitors of GSK-3, to evaluate the impact of alignment on statistical performances of the Quantitative Structure-Activity Relationship (QSAR) and the effect of the template on shape-similarity--binding affinity relationship. MATERIALS AND METHODS Dragon descriptors were used to generate Projection to Latent Structures (PLS) models in order to identify the structural prerequisites of maleimides to inhibit GSK-3. Additionally, shape/volume structural analysis of binding site interactions was evaluated. RESULTS Reliable statistics R(2)(Y(CUM)) = 0.938/0.920, Q((2)(Y)(CUM)) = 0.866/0.838 for aligned and alignment free QSAR models and significant (Pearson, Kendall and Spearman) correlations between shape/volume similarity and affinities were obtained. DISCUSSION AND CONCLUSIONS The crucial structural features modulating the activity of maleimides include topology, charge, geometry, 2D autocorrelations, 3D-MoRSE as well as shape/volume and molecular flexibility.
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Affiliation(s)
- Luminita Crisan
- Department of Computational Chemistry, Institute of Chemistry of Romanian Academy , Timisoara , Romania
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Abstract
The polarizabilities and the first and second hyperpolarizabilities of 219 conjugated organic compounds are modeled by QSPR (quantitative structure activity relationship) based on a large pool of constitutional, topological, electronic and quantum chemical descriptors calculated by CODESSA Pro (comprehensive descriptors for structural and statistical analysis) derived solely from molecular structure. Multilinear models were developed using the BMLR (best multilinear regression) algorithm to relate the experimental (hyper)polarizabilities to their predicted values. The regression equations include AM1 (Austin model 1) calculated (hyper)polarizabilities together with the size, electrostatic and quantum chemical descriptors to compensate for the imprecision of the AM1 computational method. The results emphasize the main factors that influence (hyper)polarizability. All models were validated by the "leave-one-out" method and internal validations that confirmed the stability and good predictive ability.
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Affiliation(s)
- Alan R Katritzky
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
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Katritzky AR, Pacureanu L, Dobchev D, Karelson M. QSPR Study of Critical Micelle Concentration of Anionic Surfactants Using Computational Molecular Descriptors. J Chem Inf Model 2007; 47:782-93. [PMID: 17497845 DOI: 10.1021/ci600462d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A data set of 181 diverse anionic surfactants has been investigated to relate the logarithm of critical micelle concentration (cmc) to the molecular structure using Comprehensive Descriptors for Structural and Statistical Analysis (CODESSA Pro) software. A fragment approach provided superior quantitative structure-property relationship (QSPR) models in terms of statistical characteristics and predictive ability. The regression equations provided insight into the structural features of surfactants that influence cmc. The most obvious influence on cmc was manifested by hydrophobic fragments expressed by the topological and geometrical descriptors, while the hydrophilic fragment is represented by constitutional, geometrical, and charge related descriptors. Significantly important molecular descriptors in the selected QSPR models were topological, solvational, and charge-related descriptors as the driving force of the intermolecular interactions between anionic surfactants and water.
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Affiliation(s)
- Alan R Katritzky
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
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Iliescu S, Ilia G, Popa A, Dehelean G, Macarie L, Pacureanu L, Hurduc N. The study of the vapor-liquid interfacial polycondensation of the cyclohexylphosphonic dichloride with bisphenol A. Polym Bull (Berl) 2001. [DOI: 10.1007/s002890170071] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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